Moving south through Waco, the Brazos River turns from shallow rapids to flat pools, then a glassy stillness as Mustang grapes drop from low-hanging vines. Here on the riverbanks, stately oaks stand among red-brick buildings, giving Baylor University a genteel air. And as students returned to campus this week, they reveled in their home, walking the expansive quad with a lazy lope.

But amid eager reunions, hugs, and high-fives, an unsettling question lurks: How much has changed?

The murder of a student athlete this summer, evidence of corruption in the school's basketball program, and calls for President Robert Sloan's resignation have vaulted this respected but somewhat parochial Southern Baptist university into a place it's never been: the center of a national scandal. Now, the tidy lawns and columns are bearing witness to sorrow, confusion, and faith-testing questions, all in the context of unfathomable tragedy.

Most here view the death of basketball player Patrick Dennehy as an isolated incident, the result more of human frailty than institutional failure. Still, Mr. Dennehy's murder, mixed with clear evidence of wrongdoing in the athletic department, has prompted many to question their school's direction.

Like many schools nationwide, Baylor has striven for the cachet - and cash - of a top-tier reputation for athletics as well as academics and research. But the downside of that hard-won stature is seen when missteps of athletic scandal - or worse, tragedy - tarnish a school's image, as happened, too, at the University of Alabama and Iowa State University this spring. And at Baylor, tragic misteps have illuminated a struggle larger, even, than corruption within the athletic department: They've brought out a battle over the rightful mission of the university.

"Dennehy's death has been a terrible drain on everyone," says Stan Madden, a marketing professor and former head of public relations for the university. "We are a culture of inquiry here, so people are going to go over it again and again until they resolve it in their own minds."

Like most of the Baylor community, Mr. Madden watched the scandal unravel on TV this summer. When Dennehy's teammate Carlton Dotson was charged with the murder in mid-July, Madden was vacationing in Colorado. Soon after, he learned with the rest of the country that the basketball program had illegally given players gifts and scholarships.

Believing most of the story had been revealed, Madden learned a few weeks ago that coach David Bliss was secretly recorded asking players to say Dennehy earned his funds by selling drugs. The news was surreal. "It hurt everyday," says Madden. "It was like cutting a dog's tail off a little bit at a time."

Sophomore Shannon Wihlborg followed the scandal over the radio and through her parents' friends, who called after each revelation. But the news did not surprise her. "The spirit of God isn't in a lot of what's going on here," says the Katy, Tex., native, who became a Baptist a month after enrolling at Baylor.

The unethical use of money in the athletic department, she says, is an extreme example of the school's turn toward becoming a bigger, richer, more competitive institution. The cost, she says, is Baylor's spiritual mission and role as a community supporting people, not just academics.

"We're just trying to earn a reputation. Our focus should be on influencing God in all students," says Ms. Wihlborg.

She is among many members of the Baylor community who, after the summer's events, have grown apprehensive about a shift in the school's identity.

By 2012, the university aims to be ranked among the nation's top-tier institutions by recruiting high-profile faculty and more competitive students; building expensive facilities; and raising tuition, which increased 40 percent just last fall.

"We're very much in a conversation about what we want to be as an institution What does it mean to be a Christian university?" says Prof. David Corey.

At Baylor in particular, where nearly half the students are Baptist, compet-itiveness and fiscal imprudence upset many. Revelations about the basketball program using unbudgeted money to attract and retain players have exacerbated those concerns. And Dennehy's death has cast a cloud over the whole debate.

Critics say wrongdoing in the athletic department points up long-term neg-ligence. They argue that Baylor often avoids addressing problems that contradict its identity. "Baylor still thinks it's perfect, in it's own little world," says Chris Small, a senior from Houston. "[Dennehy's death] is making Baylor address reality in a way it hasn't had to."

The school's failures, critics say, result from its religious foundation, which requires a certain moral behavior - including abstaining from alcohol and sex - that many do not live up to. The consequence, they say, is a lack of support for students in need, a culture of silence and denial in which "if we don't want it to have happened, it doesn't happen," says Nabeel Uwaydah, a junior from Houston and the College of Arts & Sciences representative to the student congress.

But the flip side of those moral dictates is an atmosphere in which morality is, at least, a topic of debate. President Sloan says the university is uniquely suited to address such issues in ways other schools cannot. "Because moral education is at the heart of our mission, we can talk about these issues, I think, in a very open and direct way," he says.

Indeed, even critics say Baylor's moral mission has made it a unique place to live. "There's so much friendliness, openness, people holding doors," says senior Irene Kojevnikava from Lipetsk, Russia.

Baylor held a memorial service for Dennehy this week. During student chapel services throughout the year, several speakers will address the tragedy. The lack of other planned programs has distressed some on campus. But they also value that Baylor can discuss the issue in its own unique ways.

"As much as you love to hate Baylor, you know you wouldn't want to be anywhere else," says Mr. Uwaydah.